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Uses of Class
org.strbio.math.DMatrix

Packages that use DMatrix
org.strbio.math These classes perform functions related to mathematics and statistics. 
org.strbio.mol These classes represent objects or concepts useful to structural biologists. 
org.strbio.mol.lib These classes represent conceptual objects used in structural biology algorithms. 
org.strbio.util These classes perform general purpose utility functions. 
 

Uses of DMatrix in org.strbio.math
 

Methods in org.strbio.math that return DMatrix
static DMatrix DMatrix.add(DMatrix a, DMatrix b)
          Adds two DMatrix's and returns a new DMatrix containing the sum.
static DMatrix DMatrix.divide(DMatrix a, int b)
          Divides a DMatrix by a double, and returns a new DMatrix containing the result.
 DMatrix DMatrix.inverse()
          Returns the inverse of this matrix.
static DMatrix DMatrix.makeInverseTransform(double x, double y, double z, double phi, double theta, double psi)
          Return an inverse transformation matrix given 3 transformation coordinates and 3 Euler rotation angles.
static DMatrix DMatrix.makeTransform(double x, double y, double z, double phi, double theta, double psi)
          Return a transformation matrix given 3 transformation coordinates and 3 Euler rotation angles.
 DMatrix DMatrix.multiply(DMatrix x)
          Multiples this DMatrix by another DMatrix, and returns another DMatrix containing the result.
static DMatrix DMatrix.multiply(DMatrix a, DMatrix b)
          Multiplies two DMatrix's, and returns another DMatrix containing the result.
static DMatrix DMatrix.multiply(DMatrix a, double b)
          Multiplies a DMatrix by a double and returns a new DMatrix containing the result.
static DMatrix DMatrix.multiply(double b, DMatrix a)
          Multiplies a DMatrix by a double and returns a new DMatrix containing the result.
static DMatrix DMatrix.subtract(DMatrix a, DMatrix b)
          Subtracts one DMatrix's from another returns a new DMatrix containing the difference.
 DMatrix DVectorSet.toDMatrix()
          Return the DVector set expressed as a matrix, with one row per point, and one column per dimension.
 DMatrix DMatrix.transpose()
          Returns the transpose of this DMatrix.
 

Methods in org.strbio.math with parameters of type DMatrix
 void DMatrix.add(DMatrix x)
          Adds another DMatrix to this one.
static DMatrix DMatrix.add(DMatrix a, DMatrix b)
          Adds two DMatrix's and returns a new DMatrix containing the sum.
 double DMatrix.covar(DMatrix y)
          Returns the covariance of values in this matrix with those in another matrix.
static DMatrix DMatrix.divide(DMatrix a, int b)
          Divides a DMatrix by a double, and returns a new DMatrix containing the result.
 DMatrix DMatrix.multiply(DMatrix x)
          Multiples this DMatrix by another DMatrix, and returns another DMatrix containing the result.
 void DVector.multiply(DMatrix x)
          Multplies this DVector by a DMatrix.
static DMatrix DMatrix.multiply(DMatrix a, DMatrix b)
          Multiplies two DMatrix's, and returns another DMatrix containing the result.
static DMatrix DMatrix.multiply(DMatrix a, double b)
          Multiplies a DMatrix by a double and returns a new DMatrix containing the result.
static DVector DVector.multiply(DMatrix b, DVector a)
          Multplies a DVector by a DMatrix, and returns a new DVector with the result.
static DMatrix DMatrix.multiply(double b, DMatrix a)
          Multiplies a DMatrix by a double and returns a new DMatrix containing the result.
static DVector DVector.multiply(DVector a, DMatrix b)
          Multplies a DVector by a DMatrix, and returns a new DVector with the result.
 double DMatrix.pearson(DMatrix y)
          Returns the Pearson correlation coefficient R of values in this matrix with values in another matrix.
 void DMatrix.subtract(DMatrix x)
          Subtracts another DMatrix from this one.
static DMatrix DMatrix.subtract(DMatrix a, DMatrix b)
          Subtracts one DMatrix's from another returns a new DMatrix containing the difference.
 void DVector.transform(DMatrix x)
          transforms this vector using a transformation DMatrix.
 

Constructors in org.strbio.math with parameters of type DMatrix
DMatrix(DMatrix x)
          copies another DMatrix.
DVectorSet(DMatrix y)
          Create a set from a DMatrix, creating a new point for each row in the matrix.
 

Uses of DMatrix in org.strbio.mol
 

Fields in org.strbio.mol declared as DMatrix
 DMatrix ProfResPSI.JMCAlphaTau
          JMC's alpha/tau potential matrix.
 DMatrix ProfResPSI.JMCPhiPsi
          JMC's phi/psi potential matrix for this postion.
 

Methods in org.strbio.mol with parameters of type DMatrix
 void Atom.rotate(DMatrix rot)
          rotate an atom by multiplying by a 3x3 rotation matrix.
 void Monomer.rotate(DMatrix rot)
          rotate all atoms by multiplying by a 3x3 rotation matrix.
 void Molecule.rotate(DMatrix rot)
          rotate all atoms by multiplying by a 3x3 rotation matrix.
 void Polymer.rotate(DMatrix rot)
          rotate all monomers by multiplying by a 3x3 rotation matrix.
 void Atom.transform(DMatrix trans)
          transform the position of an atom using a 3x4 (or 4x4 with the last column constant) transformation matrix.
 void Monomer.transform(DMatrix trans)
          transform the position of all atoms.
 void Molecule.transform(DMatrix trans)
          transform the position of all atoms.
 void Polymer.transform(DMatrix trans)
          transform the position of all monomers.
 

Uses of DMatrix in org.strbio.mol.lib
 

Fields in org.strbio.mol.lib declared as DMatrix
 DMatrix PSIBlastMatrices.posFreqs
          N x 20 matrix of frequencies at each position.
 

Methods in org.strbio.mol.lib that return DMatrix
static DMatrix DayhoffMatrices.DayhoffMdm78()
          Dayhoff mutation data matrix 78.
static DMatrix DayhoffMatrices.DayhoffPam250()
           Dayhoff, MO 1978 Atlas of Protein Sequence and Structure volume 5, #3 p. 353 - 358.
static DMatrix DayhoffMatrices.DayhoffRelatednessOdds()
          Dayhoff relatedness odds matrix.
 DMatrix BackbonePotential.getHistogram(char type, int which)
          Get a raw histogram for a given residue type. 0 = all, 1 = helix, 2 = sheet, 3 = coil.
static DMatrix DayhoffMatrices.GribskovBurgess()
          g_b matrix used in: mclachlan, eisenberg - PNAS 84:4355 - 4358 Gribskov & Burgess 1986 Nucleic Acid Research vol 14 p 6745 - 6763 this is mdm78, adjusted to have mean of 0, and sd of 1.
 DMatrix BackbonePotential.makeEnergyHist(char type, double pH, double pE)
          returns energy histogram for a residue with helix probability pH, and strand probability pE.
 DMatrix BackbonePotential.makeEnergyHist(char type, double pH, double pE, double offset, double scale)
          returns energy histogram for a residue with helix probability pH, and strand probability pE.
 DMatrix MinareaResults.makeInverseTransform()
          Matrix to transform one protein on top of the other, based on the numbers from minarea.
 DMatrix MinareaResults.makeTransform()
          Matrix to transform one protein on top of the other, based on the numbers from minarea.
static DMatrix DayhoffMatrices.Mclachlan()
          mclachlan matrix described in: McLachlan Andrew D.
static DMatrix DayhoffMatrices.Sander()
          Some Sander matrix, for which I don't have the reference.
 

Uses of DMatrix in org.strbio.util
 

Methods in org.strbio.util that return DMatrix
 DMatrix DensityPlot.getMatrix()
          Returns a copy of the matrix being drawn.
 

Methods in org.strbio.util with parameters of type DMatrix
 void DensityPlot.setMatrix(DMatrix x)
          Set the matrix being drawn.
 

Constructors in org.strbio.util with parameters of type DMatrix
DensityPlot(DMatrix x, ColorScale c)
          A density plot needs a matrix and a color scale to draw it with.
 

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